diff mergevcf_wrapper.sh @ 88:c803b1068fa6 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mergevcf_wrapper.sh	Mon Feb 24 00:34:37 2014 -0500
@@ -0,0 +1,17 @@
+#!/bin/bash
+#index all vcfs
+args=""
+for file in  ${*:2}
+do
+	cp $file $file.vcf
+	java -Xmx1500m  -jar `dirname $0`/igvtools.jar index $file.vcf
+	args="$args I=$file.vcf"
+done
+
+eval java -Xmx2G -jar $JAVA_JAR_PATH/MergeVcfs.jar QUIET=True O=$1 $args
+
+for file in  ${*:2}
+do
+	rm -f $file.vcf
+	rm -f $file.vcf.idx
+done